Chlorine in PDB 6rpn: Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.

The structure of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308., PDB code: 6rpn was solved by A.Parkova, A.Lucic, J.Brem, M.A.Mcdonough, G.W.Langley, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.34 / 1.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.081, 79.155, 67.746, 90.00, 130.03, 90.00
R / Rfree (%)	12.9 / 15.6

The structure of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	6 atoms

The binding sites of Chlorine atom in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. (pdb code 6rpn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308., PDB code: 6rpn:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:14.3 occ:1.00 ZN A:ZN303 2.2 11.1 1.0 O A:HOH440 3.1 16.9 1.0 NE2 A:HIS153 3.6 12.0 1.0 CB A:ALA132 4.0 10.1 1.0 CD2 A:HIS153 4.2 9.9 1.0 CE1 A:HIS153 4.4 10.6 1.0 OH A:TYR134 4.5 13.3 1.0

Chlorine binding site 2 out of 4 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:11.2 occ:1.00 ND2 A:ASN254 3.2 21.3 0.5 ND2 A:ASN254 3.5 14.2 0.5 CA A:HIS251 3.6 9.0 1.0 ND1 A:HIS251 3.7 7.2 1.0 CB A:ASN254 3.8 11.4 0.5 CB A:ASN254 3.9 11.6 0.5 CG A:ASN254 4.0 13.2 0.5 CB A:HIS251 4.0 7.9 1.0 CG A:ASN254 4.1 19.0 0.5 O A:HOH631 4.2 22.7 1.0 CG A:HIS251 4.3 6.7 1.0 N A:HIS251 4.4 8.9 1.0 O A:HIS251 4.4 8.2 1.0 C A:HIS251 4.6 7.0 1.0 O A:LYS250 4.6 9.4 1.0 CE1 A:HIS251 4.8 9.6 1.0 C A:LYS250 4.8 10.3 1.0 O A:HOH562 4.9 11.6 1.0 OD1 A:ASN254 5.0 16.6 0.5

Chlorine binding site 3 out of 4 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:14.2 occ:1.00 ND2 B:ASN254 3.3 12.0 0.5 CA B:HIS251 3.6 10.1 1.0 CL B:CL507 3.6 19.4 1.0 ND1 B:HIS251 3.7 8.7 1.0 CB B:HIS251 3.8 10.5 1.0 CG B:HIS251 4.2 9.2 1.0 CG B:ASN254 4.3 12.8 0.5 N B:HIS251 4.3 11.0 1.0 CB B:ASN254 4.4 12.4 0.5 ND2 B:ASN254 4.4 25.1 0.5 CB B:ASN254 4.5 9.6 0.5 CG B:ASN254 4.6 21.1 0.5 O B:HIS251 4.6 10.9 1.0 C B:HIS251 4.6 9.4 1.0 O B:LYS250 4.7 11.6 1.0 O B:HOH698 4.7 20.8 1.0 C B:LYS250 4.8 12.0 1.0 CE1 B:HIS251 4.8 11.7 1.0

Chlorine binding site 4 out of 4 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl507 b:19.4 occ:1.00 ND2 B:ASN254 3.2 25.1 0.5 ND1 B:HIS251 3.3 8.7 1.0 O B:HOH602 3.4 22.8 0.5 CE1 B:HIS251 3.5 11.7 1.0 CL B:CL506 3.6 14.2 1.0 CG2 B:VAL255 4.1 13.8 1.0 CG2 B:THR206 4.2 29.3 1.0 CG B:ASN254 4.3 21.1 0.5 CB B:ASN254 4.5 12.4 0.5 CB B:ASN254 4.6 9.6 0.5 CG B:HIS251 4.6 9.2 1.0 O B:HIS251 4.6 10.9 1.0 CB B:THR206 4.7 33.9 1.0 O B:HOH699 4.7 43.6 1.0 NE2 B:HIS251 4.7 11.9 1.0 CA B:THR206 4.9 20.0 1.0

A.Parkova, A.Lucic, A.Krajnc, J.Brem, K.Calvopina, G.W.Langley, M.A.Mcdonough, P.Trapencieris, C.J.Schofield. Broad Spectrum Beta-Lactamase Inhibition By A Thioether Substituted Bicyclic Boronate. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 31841636
DOI: 10.1021/ACSINFECDIS.9B00330